Run MED

Preparation

Paths and libraries setting

# Load main packages, paths and custom functions
source("../../../source/main_packages.R")
source("../../../source/paths.R")
source("../../../source/functions.R")

# Load supplementary packages
packages <- c("Biostrings", "seqinr")
invisible(lapply(packages, require, character.only = TRUE))

Create fasta file for each Genus

To run oligotyping, we need to create fasta files for each Genus we want analyze.

Wolbachia

Asaia

Chryseobacterium

Elizabethkingia

Erwinia

Legionella

Serratia

Run Oligotyping

Wolbachia

Docker

In a terminal session :

# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/wolbachia

# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest

Alignment

# fill gaps
o-pad-with-gaps oligotyping_Wolbachia_sequences.fasta

Shannon entropy

entropy-analysis oligotyping_Wolbachia_sequences.fasta-PADDED-WITH-GAPS

Oligotyping

oligotype oligotyping_Wolbachia_sequences.fasta-PADDED-WITH-GAPS oligotyping_Wolbachia_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 2 -M 10

7 oligotypes

Asaia

Docker

In a terminal session :

# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/asaia

# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest

Alignment

# fill gaps
o-pad-with-gaps oligotyping_Asaia_sequences.fasta

Shannon entropy

entropy-analysis oligotyping_Asaia_sequences.fasta-PADDED-WITH-GAPS

Oligotyping

oligotype oligotyping_Asaia_sequences.fasta-PADDED-WITH-GAPS oligotyping_Asaia_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 5 -M 10

34 oligotypes

Chryseobacterium

Docker

In a terminal session :

# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/wolbachia

# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest

Alignment

# fill gaps
o-pad-with-gaps oligotyping_Chryseobacterium_sequences.fasta

Shannon entropy

entropy-analysis oligotyping_Chryseobacterium_sequences.fasta-PADDED-WITH-GAPS

Oligotyping

oligotype oligotyping_Chryseobacterium_sequences.fasta-PADDED-WITH-GAPS oligotyping_Chryseobacterium_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 3 -M 10

3 oligotypes

Elizabethkingia

Docker

In a terminal session :

# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/wolbachia

# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest

Alignment

# fill gaps
o-pad-with-gaps oligotyping_Elizabethkingia_sequences.fasta

Shannon entropy

entropy-analysis oligotyping_Elizabethkingia_sequences.fasta-PADDED-WITH-GAPS

Oligotyping

oligotype oligotyping_Elizabethkingia_sequences.fasta-PADDED-WITH-GAPS oligotyping_Elizabethkingia_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 1 -M 10

2 oligotypes

Erwinia

Docker

In a terminal session :

# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/wolbachia

# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest

Alignment

# fill gaps
o-pad-with-gaps oligotyping_Erwinia_sequences.fasta

Shannon entropy

entropy-analysis oligotyping_Erwinia_sequences.fasta-PADDED-WITH-GAPS

Oligotyping

oligotype oligotyping_Erwinia_sequences.fasta-PADDED-WITH-GAPS oligotyping_Erwinia_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 8 -M 10

9 oligotypes

Legionella

Docker

In a terminal session :

# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/wolbachia

# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest

Alignment

# fill gaps
o-pad-with-gaps oligotyping_Legionella_sequences.fasta

Shannon entropy

entropy-analysis oligotyping_Legionella_sequences.fasta-PADDED-WITH-GAPS

Oligotyping

oligotype oligotyping_Legionella_sequences.fasta-PADDED-WITH-GAPS oligotyping_Legionella_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 4 -M 10

4 oligotypes

Serratia

Docker

In a terminal session :

# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/wolbachia

# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest

Alignment

# fill gaps
o-pad-with-gaps oligotyping_Serratia_sequences.fasta

Shannon entropy

entropy-analysis oligotyping_Serratia_sequences.fasta-PADDED-WITH-GAPS

Oligotyping

oligotype oligotyping_Serratia_sequences.fasta-PADDED-WITH-GAPS oligotyping_Serratia_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 1 -M 10

2 oligotypes